GIDE Metadata Snapshot (D10.1)

Harmonized study-level metadata from three major bioimaging repositories — BioImage Archive (BIA), Image Data Resource (IDR), and SSBD — in one FAIR, queryable dataset.

• 📦 Data: https://zenodo.org/records/20922775
• 📄 Report (D10.1): https://zenodo.org/records/20807591

See also https://www.gide-project.org/portal for the data usage in GIDE.

What's inside

• > 1000 studies, each as a JSON-LD RO-Crate (detached, v1.2)
• A combined RDF graph (Turtle) of all studies
• A SHACL shape for validating against the GIDE RO-Crate profile
• Species and imaging methods annotated with NCBI Taxonomy and FBbi ontology terms
• Example SPARQL queries and a ready-to-run local endpoint

Files

File	Description
gide_profile.md	Human-readable profile specification
gide_profile_shacl_shape.ttl	Machine-readable profile (SHACL)
gide_metadata_combined.ttl	All RO-Crates merged into one RDF graph
gide_metadata_with_ontologies.ttl	Combined graph + FBbi/NCBITaxon parent terms for hierarchical search
gide_profile_validation.html	SHACL validation report
gide_ncbi_and_fbbi_validation.html	Ontology term/label consistency report
gide_sparnatural_template.ttl	Config for the Sparnatural visual query UI
Qleverfile	Local SPARQL endpoint setup (QLever)
Qleverfile-ui.yml	QLever UI config with example queries

Data model (minimum)

Each study is a schema:Dataset that must link to:

• schema:about → the species studied (NCBI Taxonomy term recommended)
• measurementMethod → the imaging method (FBbi term recommended)

The full profile (aligned with REMBI) supports richer biosample, method, and descriptive metadata. See D7.1 for details.

Metadata is study-level only; direct file download links are not included.

Quick start (RDF graph)

1. Download the files from Zenodo.
2. Install QLever.
3. Run qlever index, then qlever start using the provided Qleverfile.
4. Launch the UI with Qleverfile-ui.yml and try the example queries.

Example query

Find studies by species and imaging method:

SELECT DISTINCT ?studyName ?identifier ?species ?imagingMethod
WHERE {
  ?study a schema:Dataset ;
         schema:name ?studyName ;
         schema:identifier ?identifier ;
         schema:about ?species ;
         dwc:measurementMethod ?imagingMethod .
}

Source pipelines

• BIA: https://github.com/BioImage-Archive/gide-ro-crate
• IDR: https://github.com/German-BioImaging/idr_study_crates
• SSBD: https://github.com/openssbd/gide-ro-crate

This repository harvests, validates, and combines their outputs.

References

• D10.1: Harmonized metadata snapshot (this deliverable) — https://zenodo.org/records/20807591
• D6.1: Metadata model overlap and gaps — https://doi.org/10.5281/zenodo.16794787
• D7.1: Minimal shared interoperability metadata set — https://doi.org/10.5281/zenodo.20808012